BatchBrainMRTumorSegmentation

[saimasafdar2021]

does tumor segmentation for a batch using T1, T1c, flair and T2 images. It uses the brats toolkit to perform segmentation. Its a wrapper for brats toolkit for performing batch processing.

New extension

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[saimasafdar2021]

Hi,
Is there anything on my side to do for publishing it with 3D Slicer. When I can see it in the slicer extension wizard? I have written a publication regarding this extension which requires it to be published first. We are sending the Publication to SoftwareX journal. Could you please send update on this publishing of this extension.

Thank you

regards,
Saima

[pieper]

I didn't try the code, but a few small notes from a quick look:

• You say brats needs to be installed in a different python but you don't give any details about it. This isn't a common way to distribute software for slicer so some information for users would help. Does that other tool require a GPU? Does it work on all platforms? You need to provide links to the required software.
• You have some extra python files in the same directory with you scripted module source code. Those will probably be loaded to test for modules and generate warnings. It's not clear from a quick look what those do so they should be removed or moved.
• There is a pycache folder in your repo that should probably not be in git.

[saimasafdar2021]

Hi,
I have made the changes required.
I have added the link to install the brats-toolkit and other installations suchas nvidia.
I have removed the folder pycache
I have made the scripted files to another folder. These files are required by the program from within the module.

regards,
Saima

[pieper]

Does anyone else want to have a look at this before merging? @lassoan @jcfr ?

[saimasafdar2021]

Please recommend any changes if required.

many thanks.

regards,
Saima

[saimasafdar2021]

Hi,
I am writing to know the status of this extension. Please let me know if I need to change anything to get it published.

regards,
Saima

[lassoan]

Sorry for the delayed feeback.

The extension cannot be built or packaged, because it does not follow the extension template. The most important thing is that the top-level CMakeLists.txt file is missing!!

You can use the Extension Wizard module in Slicer to create a valid extension template and add those files to your repository.

Also note that the .s4ext file is corrupted (contributors field is missing, field name of description field is missing, there may be other issues as well). I would recommend to build 3D Slicer and then build your extension to test that it can be built and packaged successfully and then you also get an .s4ext file in your build tree that you can use in this pull request (just modify scmrevision to main). If you are unable to build Slicer then you must really, really carefully copy all the content from any other extension's s4ext file and update it to match the contents of the top-level CMakeLists.txt file in your repository.

[saimasafdar2021]

Hi Andras,
I have made the changes you suggested. Carefully copied the .s4ext file and checked all required fields. I have created the cmakeList.txt file and is consistent with the contents in the .s4ext file.

Please let me know if there are any other requirements.

thank you so much.

regards,
Saima

[jcfr]

Unable to force push changes onto UWA-Medical-Physics/ExtensionsIndex@main, the updated changes are published here main...jcfr:ExtensionsIndex:UWA-Medical-Physics-main

Consider running the following command to update this pull request:

git clone [email protected]:UWA-Medical-Physics/ExtensionsIndex.git
cd ExtensionsIndex
git checkout main
git remote add jcfr https://github.com/jcfr/ExtensionsIndex.git
git fetch jcfr
git reset --hard jcfr/UWA-Medical-Physics-main
git push origin main --force

[jcfr]

Consider address the following issue:

• Ensure bratsFusionator/bratsPreprocessor/bratsSegmentor are distributed UWA-Medical-Physics/SlicerBatchBrainMRTumorSegmentation#2

[saimasafdar2021]

Hi Jean,
I have successfully submitted the extension as asked.
Create SlicerBrats.json #2069

regards,
Saima

[saimasafdar2021]

Consider address the following issue:

* [Ensure bratsFusionator/bratsPreprocessor/bratsSegmentor are distributed UWA-Medical-Physics/SlicerBatchBrainMRTumorSegmentation#2](https://github.com/UWA-Medical-Physics/SlicerBatchBrainMRTumorSegmentation/issues/2)

Hi Jean,
I have successfully submitted the extension as asked.
Create SlicerBrats.json #2069

regards,
Saima